darB
168
[metabolite|c-di-AMP] binding protein, stimulates (p)[metabolite|ppGpp] accumulation under conditions of potassium starvation
locus
BSU_14130
Molecular weight
16.49 kDa
pI
5.16
function
control of [protein|CEE73284EFC0DBE8870CE0B474922DED79475A57|rel] activity, trigger of the stringent response under conditions of potassium starvation
product
[metabolite|c-di-AMP] binding protein
essential
no
synonyms
darB, ykuL
Outlinks
Genomic Context
Categories containing this gene/protein
List of homologs in different organisms
This gene is a member of the following regulons
Gene
Coordinates
1,485,453 1,485,896
Phenotypes of a mutant
inactivation of [gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB] facilitates the adaptation of a strain lacking [metabolite|c-di-AMP] to growth on complex medium [pubmed|33481774]
The protein
Catalyzed reaction/ biological activity
apo-[protein|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB] (under conditions of [metabolite|potassium] starvation) binds to [protein|CEE73284EFC0DBE8870CE0B474922DED79475A57|rel] to trigger (p)[metabolite|ppGpp] accumulation [pubmed|33619274]
[wiki|Domains]
[wiki|CBS domain] (aa 18-78) (according to UniProt)
Structure
[PDB|6YJ8] (Apo-DarB) [pubmed|35714772]
[PDB|6YJA] (complex with [metabolite|c-di-AMP]) [pubmed|35714772]
[PDB|8ACU] (the [protein|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]2-[protein|CEE73284EFC0DBE8870CE0B474922DED79475A57|rel]NTD2 complex) [pubmed|36652515]
[AF|O31698]
Effectors of protein activity
binds [metabolite|c-di-AMP] [pubmed|33619274,31061098], this prevents binding to [protein|CEE73284EFC0DBE8870CE0B474922DED79475A57|rel] [pubmed|33619274]
Expression and Regulation
Operons
genes
[gene|A26502ADAC214D45A8F7F394587B0BDFBE7AF28E|ykuJ]-[gene|7FD784C885605F7FD27898BC9E83C28F21BE0E9D|ykuK]-[gene|899FF5BEE5D3F01778A0175E293EDBBDEB25717D|abbA]-[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]-[gene|FE15A41A58A8177280817CA3825764C39185021A|ccpC]
description
[Pubmed|16395550]
regulation
expressed under conditions that trigger sporulation ([wiki|Spo0A]) [Pubmed|14651647]
regulatory mechanism
[protein|2C54FE2ADC82FF414D732018C90649D477A925AD|spo0A]: activation, by [protein|2C54FE2ADC82FF414D732018C90649D477A925AD|spo0A]~P [Pubmed|18840696,14651647], in [regulon|protein:2C54FE2ADC82FF414D732018C90649D477A925AD|spo0A regulon]
[protein|E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|ccpA]: repression, [Pubmed|16395550,12850135], in [regulon|protein:E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|ccpA regulon]
Biological materials
Mutant
MGNA-A773 (darB::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/773 NBRP B. subtilis, Japan]
GP2769 (Δ[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]::erm) available in [wiki|Jörg Stülke]'s lab
GP3409(Δ[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]::cat) available in [wiki|Jörg Stülke]'s lab
BKE14130 (''darB''::''erm trpC2'') available in the Bacillus Genetic Stock Center and in [wiki|Jörg Stülke]'s lab [pubmed|28189581]
GP214 (deletion of [gene|A26502ADAC214D45A8F7F394587B0BDFBE7AF28E|ykuJ]-[gene|7FD784C885605F7FD27898BC9E83C28F21BE0E9D|ykuK]-[gene|899FF5BEE5D3F01778A0175E293EDBBDEB25717D|abbA]-[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB], replaced by ''kan''), available in [wiki|Jörg Stülke]'s lab
BKE14130 ([gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]::erm trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKE14130 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATGTTTTCGACCCCTTTTC, downstream forward: _UP4_TAGGCTGTACGGTCCTATTT
BKK14130 ([gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]::kan trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKK14130 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATGTTTTCGACCCCTTTTC, downstream forward: _UP4_TAGGCTGTACGGTCCTATTT
GP2800 (Δ[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]-[gene|FE15A41A58A8177280817CA3825764C39185021A|ccpC]::phleo), available in [wiki|Jörg Stülke]'s lab
Expression vectors
pGP2929 (N-terminal 6xHis-tag, purification from E. coli, in [wiki|pWH844]), available in [wiki|Jörg Stülke]'s lab
pGP2972 (N-terminal 6xHis-SUMO-tag, purification from E. coli, in pET-SUMO), available in [wiki|Jörg Stülke]'s lab
pGP635: expression of Strep-[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB] by [wiki|pGP380] in B. subtilis suitable for [wiki|SPINE], available in [wiki|Jörg Stülke]'s lab
pGP767: expression of [gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]-Strep by [wiki|pGP382] in B. subtilis suitable for [wiki|SPINE], available in [wiki|Jörg Stülke]'s lab
pGP3306: expression of [gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB] by [wiki|pBQ200] in B. subtilis, available in [wiki|Jörg Stülke]'s lab
two-hybrid system
B. pertussis adenylate cyclase-based bacterial two hybrid system ([wiki|BACTH]), available in [wiki|Jörg Stülke]'s lab
FLAG-tag construct
GP2810 [gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]-3xFLAG spc (based on [wiki|pGP1331]), available in [wiki|Jörg Stülke]'s lab
labs
[wiki|Jörg Stülke], University of Göttingen, Germany [http://genmibio.uni-goettingen.de Homepage]
References
Reviews
Original Publications
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Time of last update: 2024-11-20 19:46:08
Author of last update: Dennis.wicke